Cited by 1,088CRISPR and Genetic EngineeringRNA regulation and diseaseRNA Interference and Gene Delivery

CCTop: An intuitive, flexible and reliable CRISPR/Cas9 target prediction tool

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Stemmer, Manuel, Thumberger, Thomas, del Sol Keyer, Maria, Wittbrodt, Joachim, Mateo, Juan L.·2015·PLoS ONE

Abstract

Engineering of the CRISPR/Cas9 system has opened a plethora of new opportunities for site-directed mutagenesis and targeted genome modification. Fundamental to this is a stretch of twenty nucleotides at the 5' end of a guide RNA that provides specificity to the bound Cas9 endonuclease. Since a sequence of twenty nucleotides can occur multiple times in a given genome and some mismatches seem to be accepted by the CRISPR/Cas9 complex, an efficient and reliable in silico selection and evaluation of the targeting site is key prerequisite for the experimental success. Here we present the CRISPR/Cas9 target online predictor (CCTop, http://crispr.cos.uni-heidelberg.de) to overcome limitations of already available tools. CCTop provides an intuitive user interface with reasonable default parameters that can easily be tuned by the user. From a given query sequence, CCTop identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. CCTop was experimentally validated for gene inactivation, non-homologous end-joining as well as homology directed repair. Thus, CCTop provides the bench biologist with a tool for the rapid and efficient identification of high quality target sites.

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  • CCTop and CROP-IT generate scores based on the distances of the mismatches to the PAM.

    “CCTop and CROP-IT generate scores based on the distances of the mismatches to the PAM (Singh et al., 2015; Stemmer et al., 2015).”

    From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Stemmer et al., 2015

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Authors
Stemmer, M., Thumberger, T., del Sol Keyer, M., Wittbrodt, J., & Mateo, J. L.
Affiliations
Heidelberg University (DE)
Corresponding author
  • Thumberger, Thomas
  • Wittbrodt, Joachim
  • Mateo, Juan L.
Venue
PLoS ONE
Published
2015-04-24
Volume
10
Issue
4
Pages
e0124633
ISSN
1932-6203 (ISSN-L)
OpenAlex
W1990149668
Cited by
1,088
References
37
Citations by year
2026: 87 · 2025: 99 · 2024: 106 · 2023: 140 · 2022: 129 · 2021: 114 · 2020: 139 · 2019: 96 · 2018: 72 · 2017: 53 · 2016: 39 · 2015: 13
FWCI
25.61
Type
journal article
Language
en
Open access
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Figshare (submittedVersion, cc-by)
Funders
  • Deutsche Forschungsgemeinschaft (SFB873)
  • Universität Heidelberg
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
Keywords
CRISPR/Cas9, sgRNA design, off-target prediction, genome editing, gene inactivation, non-homologous end joining, homology-directed repair, web-based prediction tool
MeSH terms
Animals, Binding Sites, Humans, RNA, Messenger, Software, User-Computer Interface, Reproducibility of Results, Gene Targeting, Computational Biology, Internet, Genomics, CRISPR-Cas Systems, Web Browser

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